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IsoEM2 estimates fragments per kilobase million (FPKM) and transcript per million (TPM) levels for genes and isoforms with confidence intervals through bootstrapping, while IsoDE2 performs differential expression analysis using the bootstrap samples generated by IsoEM2. Both tools are available with a command line interface as well as a graphical user interface (GUI) through wrappers for the Galaxy platform.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code of this software suite is available at https:\/\/github.com\/mandricigor\/isoem2. The Galaxy wrappers are available at https:\/\/toolshed.g2.bx.psu.edu\/view\/saharlcc\/isoem2_isode2\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx365","type":"journal-article","created":{"date-parts":[[2017,6,7]],"date-time":"2017-06-07T03:11:55Z","timestamp":1496805115000},"page":"3302-3304","source":"Crossref","is-referenced-by-count":51,"title":["Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data"],"prefix":"10.1093","volume":"33","author":[{"given":"Igor","family":"Mandric","sequence":"first","affiliation":[{"name":"Department of Computer Science, Georgia State University, Atlanta, GA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yvette","family":"Temate-Tiagueu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Georgia State University, Atlanta, GA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatiana","family":"Shcheglova","sequence":"additional","affiliation":[{"name":"Immunology Department, University of Connecticut Health Center, Farmington, CT, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sahar","family":"Al Seesi","sequence":"additional","affiliation":[{"name":"Immunology Department, University of Connecticut Health Center, Farmington, CT, USA"},{"name":"Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Zelikovsky","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Georgia State University, Atlanta, GA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ion I","family":"M\u0103ndoiu","sequence":"additional","affiliation":[{"name":"Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,6,10]]},"reference":[{"key":"2023020301105317800_btx365-B1","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2164-15-S8-S2","article-title":"Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates","volume":"15(Suppl 8)","author":"Al Seesi","year":"2014","journal-title":"BMC Genomics"},{"key":"2023020301105317800_btx365-B2","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal RNA-Seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. 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